scafari

Analysis of scDNA-seq data

Bioconductor version: 3.23 · Package version: 1.2.0

Scafari is a Shiny application designed for the analysis of single-cell DNA sequencing (scDNA-seq) data provided in .h5 file format. The analysis process is structured into the four key steps "Sequencing", "Panel", "Variants", and "Explore Variants". It supports various analyses and visualizations.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scafari")

Details

Maintainer	Sophie Wind <sophie.wind@uni-muenster.de>
Author	Sophie Wind [aut, cre] (ORCID: <https://orcid.org/0009-0002-1174-8201>)
License	LGPL-3
URL	https://github.com/sophiewind/scafari
Bug Reports	https://github.com/sophiewind/scafari/issues
Downloads rank	160
Source branch	RELEASE_3_23
biocViews	Sequencing, ShinyApps, SingleCell, Software

Documentation

scafari_vignette

Download

Source package

Dependencies

Depends: R (>= 4.5.0)

Imports: magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2, tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader, factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5, ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment, SingleCellExperiment, S4Vectors, parallel, httr, jsonlite, scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph, RANN

Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)